I am assuming I would need to run minimization for explicit solvent and periodic boundary should be enable as shown here:
http://ambermd.org/tutorials/basic/tutorial1/section5.htm
I shall try this out.
Thanks for suggestions !
AG
________________________________________
From: David A Case [case.biomaps.rutgers.edu]
Sent: Wednesday, December 17, 2014 2:17 PM
To: AMBER Mailing List
Subject: Re: [AMBER] error running equilibration (wall clock called)
On Wed, Dec 17, 2014, Anupam Goel wrote:
>
> I am trying to run a simulation on peptide linked to APD-ribose
> (following tutorial advanced tut 1_orig). I was able to save the
> prmtop and inpcrd files. After performing heating, equilibration shows
> MPI_Abort process 0.
Be sure you can carry out serial calcualtions before trying parallel ones.
>
> equil.out looks as below and says "wall clock was called"
This looks like a normal termination of the job. There are no errors that
I can see. But the job only ran for 11 sec--maybe there is some information
earlier in the file that would help.
....dac
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Received on Wed Dec 17 2014 - 14:00:02 PST
